Commit 946ea4c2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed outputDirs

parent 60fc26c3
...@@ -57,7 +57,10 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript ...@@ -57,7 +57,10 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
require(inputBams.nonEmpty, "No input bams found") require(inputBams.nonEmpty, "No input bams found")
require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", ")) require(callers.nonEmpty, "must select at least 1 SV caller, choices are: " + callersList.map(_.name).mkString(", "))
callers.foreach(add) callers.foreach { caller =>
caller.outputDir = new File(outputDir, caller.name)
add(caller)
}
addSummaryJobs() addSummaryJobs()
} }
......
...@@ -87,6 +87,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript ...@@ -87,6 +87,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript
for (caller <- callers) { for (caller <- callers) {
caller.inputBams = inputBams caller.inputBams = inputBams
caller.namePrefix = namePrefix caller.namePrefix = namePrefix
caller.outputDir = new File(outputDir, caller.name)
add(caller) add(caller)
addStats(caller.outputFile, caller.name) addStats(caller.outputFile, caller.name)
val normalize: Boolean = config("execute_vt_normalize", default = false, submodule = caller.configName) val normalize: Boolean = config("execute_vt_normalize", default = false, submodule = caller.configName)
......
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